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Recommendations for calling on and flitering ~100 low coverage samples

I have about 80-100 population-specific WGS samples with coverage around 5-10X. What modifications would you recommend in GATK best practices to suit variant calling (and VQSR) ? Also, what are the drawbacks of using the standard GVCF joint genotyping workflow for low coverage samples ?

I have one high coverage sample of about 30X; Would it help if I pool that in ?

Answers

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